2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignSeq;
24 import jalview.appletgui.AlignmentPanel;
25 import jalview.appletgui.FeatureRenderer;
26 import jalview.appletgui.SequenceRenderer;
27 import jalview.datamodel.PDBEntry;
28 import jalview.datamodel.SequenceI;
29 import jalview.io.DataSourceType;
30 import jalview.io.StructureFile;
31 import jalview.renderer.seqfeatures.FeatureColourFinder;
32 import jalview.structure.AtomSpec;
33 import jalview.structure.StructureListener;
34 import jalview.structure.StructureMapping;
35 import jalview.structure.StructureSelectionManager;
36 import jalview.util.MessageManager;
38 import java.awt.Color;
39 import java.awt.Dimension;
40 import java.awt.Event;
42 import java.awt.Graphics;
43 import java.awt.Image;
44 // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
45 import java.awt.Panel;
46 import java.awt.event.KeyAdapter;
47 import java.awt.event.KeyEvent;
48 import java.awt.event.MouseEvent;
49 import java.awt.event.MouseListener;
50 import java.awt.event.MouseMotionListener;
51 import java.io.PrintStream;
52 import java.util.List;
53 import java.util.Vector;
55 public class AppletPDBCanvas extends Panel implements MouseListener,
56 MouseMotionListener, StructureListener
59 MCMatrix idmat = new MCMatrix(3, 3);
61 MCMatrix objmat = new MCMatrix(3, 3);
63 boolean redrawneeded = true;
73 public StructureFile pdb;
85 float[] centre = new float[3];
87 float[] width = new float[3];
97 boolean bysequence = true;
99 boolean depthcue = true;
101 boolean wire = false;
103 boolean bymolecule = false;
105 boolean zbuffer = true;
121 Font font = new Font("Helvetica", Font.PLAIN, 10);
123 public SequenceI[] sequence;
125 final StringBuffer mappingDetails = new StringBuffer();
127 String appletToolTip = null;
133 Vector<String> highlightRes;
135 boolean pdbAction = false;
137 Bond highlightBond1, highlightBond2;
139 boolean errorLoading = false;
141 boolean seqColoursReady = false;
147 StructureSelectionManager ssm;
149 public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
150 String[] chains, AlignmentPanel ap, DataSourceType protocol)
154 this.pdbentry = pdbentry;
157 ssm = StructureSelectionManager
158 .getStructureSelectionManager(ap.av.applet);
162 pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
164 if (protocol == DataSourceType.PASTE)
166 pdbentry.setFile("INLINE" + pdb.getId());
169 } catch (Exception ex)
171 ex.printStackTrace();
175 pdbentry.setId(pdb.getId());
177 ssm.addStructureViewerListener(this);
188 // JUST DEAL WITH ONE SEQUENCE FOR NOW
189 SequenceI sequence = seq[0];
191 for (int i = 0; i < pdb.getChains().size(); i++)
195 .append("\n\nPDB Sequence is :\nSequence = "
196 + pdb.getChains().elementAt(i).sequence
197 .getSequenceAsString());
198 mappingDetails.append("\nNo of residues = "
199 + pdb.getChains().elementAt(i).residues.size() + "\n\n");
201 // Now lets compare the sequences to get
202 // the start and end points.
203 // Align the sequence to the pdb
204 // TODO: DNa/Pep switch
205 AlignSeq as = new AlignSeq(sequence,
206 pdb.getChains().elementAt(i).sequence, pdb.getChains()
207 .elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
208 as.calcScoreMatrix();
210 PrintStream ps = new PrintStream(System.out)
213 public void print(String x)
215 mappingDetails.append(x);
219 public void println()
221 mappingDetails.append("\n");
225 as.printAlignment(ps);
227 if (as.maxscore > max)
232 pdbstart = as.seq2start;
234 seqstart = as.seq1start + sequence.getStart() - 1;
235 seqend = as.seq1end + sequence.getEnd() - 1;
238 mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
239 mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
242 mainchain = pdb.getChains().elementAt(maxchain);
244 mainchain.pdbstart = pdbstart;
245 mainchain.pdbend = pdbend;
246 mainchain.seqstart = seqstart;
247 mainchain.seqend = seqend;
248 mainchain.isVisible = true;
249 // mainchain.makeExactMapping(maxAlignseq, sequence);
250 // mainchain.transferRESNUMFeatures(sequence, null);
252 this.prefsize = new Dimension(getSize().width, getSize().height);
254 // Initialize the matrices to identity
255 for (int i = 0; i < 3; i++)
257 for (int j = 0; j < 3; j++)
261 idmat.addElement(i, j, 0);
262 objmat.addElement(i, j, 0);
266 idmat.addElement(i, j, 1);
267 objmat.addElement(i, j, 1);
272 addMouseMotionListener(this);
273 addMouseListener(this);
275 addKeyListener(new KeyAdapter()
278 public void keyPressed(KeyEvent evt)
292 Vector<Bond> visiblebonds;
296 seqColoursReady = false;
297 // Sort the bonds by z coord
298 visiblebonds = new Vector<Bond>();
300 for (int ii = 0; ii < pdb.getChains().size(); ii++)
302 if (pdb.getChains().elementAt(ii).isVisible)
304 Vector<Bond> tmp = pdb.getChains().elementAt(ii).bonds;
306 for (int i = 0; i < tmp.size(); i++)
308 visiblebonds.addElement(tmp.elementAt(i));
312 seqColoursReady = true;
318 public void findWidth()
320 float[] max = new float[3];
321 float[] min = new float[3];
323 max[0] = (float) -1e30;
324 max[1] = (float) -1e30;
325 max[2] = (float) -1e30;
327 min[0] = (float) 1e30;
328 min[1] = (float) 1e30;
329 min[2] = (float) 1e30;
331 for (int ii = 0; ii < pdb.getChains().size(); ii++)
333 if (pdb.getChains().elementAt(ii).isVisible)
335 Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
337 for (Bond tmp : bonds)
339 if (tmp.start[0] >= max[0])
341 max[0] = tmp.start[0];
344 if (tmp.start[1] >= max[1])
346 max[1] = tmp.start[1];
349 if (tmp.start[2] >= max[2])
351 max[2] = tmp.start[2];
354 if (tmp.start[0] <= min[0])
356 min[0] = tmp.start[0];
359 if (tmp.start[1] <= min[1])
361 min[1] = tmp.start[1];
364 if (tmp.start[2] <= min[2])
366 min[2] = tmp.start[2];
369 if (tmp.end[0] >= max[0])
374 if (tmp.end[1] >= max[1])
379 if (tmp.end[2] >= max[2])
384 if (tmp.end[0] <= min[0])
389 if (tmp.end[1] <= min[1])
394 if (tmp.end[2] <= min[2])
402 width[0] = Math.abs(max[0] - min[0]);
403 width[1] = Math.abs(max[1] - min[1]);
404 width[2] = Math.abs(max[2] - min[2]);
408 if (width[1] > width[0])
413 if (width[2] > width[1])
418 // System.out.println("Maxwidth = " + maxwidth);
421 public float findScale()
427 if (getSize().width != 0)
429 width = getSize().width;
430 height = getSize().height;
434 width = prefsize.width;
435 height = prefsize.height;
447 return (float) (dim / (1.5d * maxwidth));
450 public void findCentre()
458 // Find centre coordinate
459 for (int ii = 0; ii < pdb.getChains().size(); ii++)
461 if (pdb.getChains().elementAt(ii).isVisible)
463 Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
465 bsize += bonds.size();
469 xtot = xtot + b.start[0] + b.end[0];
470 ytot = ytot + b.start[1] + b.end[1];
471 ztot = ztot + b.start[2] + b.end[2];
476 centre[0] = xtot / (2 * (float) bsize);
477 centre[1] = ytot / (2 * (float) bsize);
478 centre[2] = ztot / (2 * (float) bsize);
482 public void paint(Graphics g)
487 g.setColor(Color.white);
488 g.fillRect(0, 0, getSize().width, getSize().height);
489 g.setColor(Color.black);
490 g.setFont(new Font("Verdana", Font.BOLD, 14));
492 MessageManager.getString("label.error_loading_pdb_data"), 50,
493 getSize().height / 2);
497 if (!seqColoursReady)
499 g.setColor(Color.black);
500 g.setFont(new Font("Verdana", Font.BOLD, 14));
501 g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50,
502 getSize().height / 2);
506 // Only create the image at the beginning -
507 // this saves much memory usage
508 if ((img == null) || (prefsize.width != getSize().width)
509 || (prefsize.height != getSize().height))
514 prefsize.width = getSize().width;
515 prefsize.height = getSize().height;
518 img = createImage(prefsize.width, prefsize.height);
519 ig = img.getGraphics();
522 } catch (Exception ex)
524 ex.printStackTrace();
530 drawAll(ig, prefsize.width, prefsize.height);
531 redrawneeded = false;
533 if (appletToolTip != null)
535 ig.setColor(Color.red);
536 ig.drawString(appletToolTip, toolx, tooly);
539 g.drawImage(img, 0, 0, this);
544 public void drawAll(Graphics g, int width, int height)
546 ig.setColor(Color.black);
547 ig.fillRect(0, 0, width, height);
552 public void setColours(jalview.schemes.ColourSchemeI cs)
560 // This method has been taken out of PDBChain to allow
561 // Applet and Application specific sequence renderers to be used
562 void colourBySequence()
564 SequenceRenderer sr = new SequenceRenderer(ap.av);
566 StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
568 boolean showFeatures = false;
569 if (ap.av.isShowSequenceFeatures())
573 fr = new jalview.appletgui.FeatureRenderer(ap.av);
576 fr.transferSettings(ap.getFeatureRenderer());
581 FeatureColourFinder finder = new FeatureColourFinder(fr);
584 if (bysequence && pdb != null)
586 for (int ii = 0; ii < pdb.getChains().size(); ii++)
588 chain = pdb.getChains().elementAt(ii);
590 for (int i = 0; i < chain.bonds.size(); i++)
592 Bond tmp = chain.bonds.elementAt(i);
593 tmp.startCol = Color.lightGray;
594 tmp.endCol = Color.lightGray;
595 if (chain != mainchain)
600 for (int s = 0; s < sequence.length; s++)
602 for (int m = 0; m < mapping.length; m++)
604 if (mapping[m].getSequence() == sequence[s])
606 int pos = mapping[m].getSeqPos(tmp.at1.resNumber) - 1;
609 pos = sequence[s].findIndex(pos);
610 tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
613 tmp.startCol = finder.findFeatureColour(tmp.startCol,
617 pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
620 pos = sequence[s].findIndex(pos);
621 tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
624 tmp.endCol = finder.findFeatureColour(tmp.endCol,
638 public void drawScene(Graphics g)
647 zsort.sort(visiblebonds);
651 for (int i = 0; i < visiblebonds.size(); i++)
653 tmpBond = visiblebonds.elementAt(i);
655 xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
656 ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
658 xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
659 yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getSize().height / 2));
661 xmid = (xend + xstart) / 2;
662 ymid = (yend + ystart) / 2;
664 if (depthcue && !bymolecule)
666 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
668 g.setColor(tmpBond.startCol.darker().darker());
669 drawLine(g, xstart, ystart, xmid, ymid);
671 g.setColor(tmpBond.endCol.darker().darker());
672 drawLine(g, xmid, ymid, xend, yend);
674 else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
676 g.setColor(tmpBond.startCol.darker());
677 drawLine(g, xstart, ystart, xmid, ymid);
679 g.setColor(tmpBond.endCol.darker());
680 drawLine(g, xmid, ymid, xend, yend);
684 g.setColor(tmpBond.startCol);
685 drawLine(g, xstart, ystart, xmid, ymid);
687 g.setColor(tmpBond.endCol);
688 drawLine(g, xmid, ymid, xend, yend);
692 else if (depthcue && bymolecule)
694 if (tmpBond.start[2] < (centre[2] - (maxwidth / 6)))
696 g.setColor(Color.green.darker().darker());
697 drawLine(g, xstart, ystart, xend, yend);
699 else if (tmpBond.start[2] < (centre[2] + (maxwidth / 6)))
701 g.setColor(Color.green.darker());
702 drawLine(g, xstart, ystart, xend, yend);
706 g.setColor(Color.green);
707 drawLine(g, xstart, ystart, xend, yend);
710 else if (!depthcue && !bymolecule)
712 g.setColor(tmpBond.startCol);
713 drawLine(g, xstart, ystart, xmid, ymid);
714 g.setColor(tmpBond.endCol);
715 drawLine(g, xmid, ymid, xend, yend);
719 drawLine(g, xstart, ystart, xend, yend);
722 if (highlightBond1 != null && highlightBond1 == tmpBond)
724 g.setColor(Color.white);
725 drawLine(g, xmid, ymid, xend, yend);
728 if (highlightBond2 != null && highlightBond2 == tmpBond)
730 g.setColor(Color.white);
731 drawLine(g, xstart, ystart, xmid, ymid);
737 public void drawLine(Graphics g, int x1, int y1, int x2, int y2)
741 if (((float) Math.abs(y2 - y1) / (float) Math.abs(x2 - x1)) < 0.5)
743 g.drawLine(x1, y1, x2, y2);
744 g.drawLine(x1 + 1, y1 + 1, x2 + 1, y2 + 1);
745 g.drawLine(x1, y1 - 1, x2, y2 - 1);
749 g.setColor(g.getColor().brighter());
750 g.drawLine(x1, y1, x2, y2);
751 g.drawLine(x1 + 1, y1, x2 + 1, y2);
752 g.drawLine(x1 - 1, y1, x2 - 1, y2);
757 g.drawLine(x1, y1, x2, y2);
761 public Dimension minimumsize()
766 public Dimension preferredsize()
771 public void doKeyPressed(KeyEvent evt)
773 if (evt.getKeyCode() == KeyEvent.VK_UP)
775 scale = (float) (scale * 1.1);
779 else if (evt.getKeyCode() == KeyEvent.VK_DOWN)
781 scale = (float) (scale * 0.9);
788 public void mousePressed(MouseEvent e)
791 Atom fatom = findAtom(e.getX(), e.getY());
794 fatom.isSelected = !fatom.isSelected;
798 if (foundchain != -1)
800 PDBChain chain = pdb.getChains().elementAt(foundchain);
801 if (chain == mainchain)
803 if (fatom.alignmentMapping != -1)
805 if (highlightRes == null)
807 highlightRes = new Vector<String>();
810 final String atomString = Integer
811 .toString(fatom.alignmentMapping);
812 if (highlightRes.contains(atomString))
814 highlightRes.removeElement(atomString);
818 highlightRes.addElement(atomString);
833 public void mouseMoved(MouseEvent e)
836 if (highlightBond1 != null)
838 highlightBond1.at2.isSelected = false;
839 highlightBond2.at1.isSelected = false;
840 highlightBond1 = null;
841 highlightBond2 = null;
844 Atom fatom = findAtom(e.getX(), e.getY());
846 PDBChain chain = null;
847 if (foundchain != -1)
849 chain = pdb.getChains().elementAt(foundchain);
850 if (chain == mainchain)
852 mouseOverStructure(fatom.resNumber, chain.id);
861 appletToolTip = chain.id + ":" + fatom.resNumber + " "
868 mouseOverStructure(-1, chain != null ? chain.id : null);
869 appletToolTip = null;
876 public void mouseClicked(MouseEvent e)
881 public void mouseEntered(MouseEvent e)
886 public void mouseExited(MouseEvent e)
891 public void mouseDragged(MouseEvent evt)
898 MCMatrix objmat = new MCMatrix(3, 3);
899 objmat.setIdentity();
901 if ((evt.getModifiers() & Event.META_MASK) != 0)
903 objmat.rotatez(((mx - omx)));
907 objmat.rotatex(((omy - my)));
908 objmat.rotatey(((omx - mx)));
912 for (PDBChain chain : pdb.getChains())
914 for (Bond tmpBond : chain.bonds)
916 // Translate the bond so the centre is 0,0,0
917 tmpBond.translate(-centre[0], -centre[1], -centre[2]);
919 // Now apply the rotation matrix
920 tmpBond.start = objmat.vectorMultiply(tmpBond.start);
921 tmpBond.end = objmat.vectorMultiply(tmpBond.end);
923 // Now translate back again
924 tmpBond.translate(centre[0], centre[1], centre[2]);
941 public void mouseReleased(MouseEvent evt)
947 void drawLabels(Graphics g)
950 for (PDBChain chain : pdb.getChains())
954 for (Bond tmpBond : chain.bonds)
956 if (tmpBond.at1.isSelected)
958 labelAtom(g, tmpBond, 1);
961 if (tmpBond.at2.isSelected)
963 labelAtom(g, tmpBond, 2);
970 public void labelAtom(Graphics g, Bond b, int n)
976 int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getSize().width / 2));
977 int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getSize().height / 2));
979 g.setColor(Color.red);
980 g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
985 int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getSize().width / 2));
986 int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getSize().height / 2));
988 g.setColor(Color.red);
989 g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
995 public Atom findAtom(int x, int y)
1001 for (int ii = 0; ii < pdb.getChains().size(); ii++)
1003 PDBChain chain = pdb.getChains().elementAt(ii);
1005 Bond tmpBond = null;
1007 if (chain.isVisible)
1009 Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
1011 for (int i = 0; i < bonds.size(); i++)
1013 tmpBond = bonds.elementAt(i);
1015 truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getSize().width / 2));
1017 if (Math.abs(truex - x) <= 2)
1019 int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getSize().height / 2));
1021 if (Math.abs(truey - y) <= 2)
1023 fatom = tmpBond.at1;
1030 // Still here? Maybe its the last bond
1032 truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getSize().width / 2));
1034 if (Math.abs(truex - x) <= 2)
1036 int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getSize().height / 2));
1038 if (Math.abs(truey - y) <= 2)
1040 fatom = tmpBond.at2;
1048 if (fatom != null) // )&& chain.ds != null)
1050 chain = pdb.getChains().elementAt(foundchain);
1058 public void update(Graphics g)
1063 public void highlightRes(int ii)
1065 if (!seqColoursReady)
1070 if (highlightRes != null && highlightRes.contains((ii - 1) + ""))
1077 for (index = 0; index < mainchain.bonds.size(); index++)
1079 tmpBond = mainchain.bonds.elementAt(index);
1080 if (tmpBond.at1.alignmentMapping == ii - 1)
1082 if (highlightBond1 != null)
1084 highlightBond1.at2.isSelected = false;
1087 if (highlightBond2 != null)
1089 highlightBond2.at1.isSelected = false;
1092 highlightBond1 = null;
1093 highlightBond2 = null;
1097 highlightBond1 = mainchain.bonds.elementAt(index - 1);
1098 highlightBond1.at2.isSelected = true;
1101 if (index != mainchain.bonds.size())
1103 highlightBond2 = mainchain.bonds.elementAt(index);
1104 highlightBond2.at1.isSelected = true;
1111 redrawneeded = true;
1115 public void setAllchainsVisible(boolean b)
1117 for (int ii = 0; ii < pdb.getChains().size(); ii++)
1119 PDBChain chain = pdb.getChains().elementAt(ii);
1120 chain.isVisible = b;
1122 mainchain.isVisible = true;
1127 // ////////////////////////////////
1128 // /StructureListener
1130 public String[] getPdbFile()
1132 return new String[] { pdbentry.getFile() };
1137 public void mouseOverStructure(int pdbResNum, String chain)
1139 if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
1141 ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
1144 lastMessage = pdbResNum + chain;
1147 StringBuffer resetLastRes = new StringBuffer();
1149 StringBuffer eval = new StringBuffer();
1152 * Highlight the specified atoms in the structure.
1157 public void highlightAtoms(List<AtomSpec> atoms)
1159 if (!seqColoursReady)
1163 for (AtomSpec atom : atoms)
1165 int atomIndex = atom.getAtomIndex();
1167 if (highlightRes != null
1168 && highlightRes.contains((atomIndex - 1) + ""))
1173 highlightAtom(atomIndex);
1176 redrawneeded = true;
1183 protected void highlightAtom(int atomIndex)
1187 for (index = 0; index < mainchain.bonds.size(); index++)
1189 tmpBond = mainchain.bonds.elementAt(index);
1190 if (tmpBond.at1.atomIndex == atomIndex)
1192 if (highlightBond1 != null)
1194 highlightBond1.at2.isSelected = false;
1197 if (highlightBond2 != null)
1199 highlightBond2.at1.isSelected = false;
1202 highlightBond1 = null;
1203 highlightBond2 = null;
1207 highlightBond1 = mainchain.bonds.elementAt(index - 1);
1208 highlightBond1.at2.isSelected = true;
1211 if (index != mainchain.bonds.size())
1213 highlightBond2 = mainchain.bonds.elementAt(index);
1214 highlightBond2.at1.isSelected = true;
1222 public Color getColour(int atomIndex, int pdbResNum, String chain,
1226 // if (!pdbfile.equals(pdbentry.getFile()))
1229 // return new Color(viewer.getAtomArgb(atomIndex));
1233 public void updateColours(Object source)
1236 redrawneeded = true;
1241 public void releaseReferences(Object svl)
1243 // TODO Auto-generated method stub
1248 public boolean isListeningFor(SequenceI seq)
1250 if (sequence != null)
1252 for (SequenceI s : sequence)